Anti-endomysial and anti-transglutaminase antibodies can be produced in vitro by the intestinal mucosa of celiac disease (CD) patients in clinical remission, when the culture is performed in the presence of gliadin peptides. Our aim was to use this organ culture system as a means to detect the pathognomonic antibodies of celiac disease (CD) in the culture supernatants. Organ culture was performed in the presence of three different activators to evaluate which one induced the strongest antibody response in intestinal mucosa from patients in clinical remission of CD. Our data confirm the high efficiency of synthetic peptide 31-43 as a specific immunological activator in CD and demonstrate its capability to stimulate production/secretion of CD-specific antibodies. We envision that this organ culture system may prove to be useful as a new technique for CD diagnosis.